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Tomioka Y, Seki N, Suetsugu T, Hagihara Y, Sanada H, Goto Y, Kikkawa N, Mizuno K, Tanaka K, Inoue H. Identification of Tumor Suppressive miR-144-5p Targets: FAM111B Expression Accelerates the Malignant Phenotypes of Lung Adenocarcinoma. Int J Mol Sci 2024; 25:9974. [PMID: 39337462 PMCID: PMC11432174 DOI: 10.3390/ijms25189974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/08/2024] [Accepted: 09/14/2024] [Indexed: 09/30/2024] Open
Abstract
Accumulating evidence suggests that the passenger strands microRNAs (miRNAs) derived from pre-miRNAs are closely involved in cancer pathogenesis. Analysis of our miRNA expression signature of lung adenocarcinoma (LUAD) and The Cancer Genome Atlas (TCGA) data revealed that miR-144-5p (the passenger strand derived from pre-miR-144) was significantly downregulated in LUAD tissues. The aim of this study was to identify therapeutic target molecules controlled by miR-144-5p in LUAD cells. Ectopic expression assays demonstrated that miR-144-5p attenuated LUAD cell aggressiveness, e.g., inhibited cell proliferation, migration and invasion abilities, and induced cell cycle arrest and apoptotic cells. A total of 18 genes were identified as putative cancer-promoting genes controlled by miR-144-5p in LUAD cells based on our in silico analysis. We focused on a family with sequence similarity 111 member B (FAM111B) and investigated its cancer-promoting functions in LUAD cells. Luciferase reporter assay showed that expression of FAM111B was directly regulated by miR-144-5p in LUAD cells. FAM111B knockdown assays showed that LUAD cells significantly suppressed malignant phenotypes, e.g., inhibited cell proliferation, migration and invasion abilities, and induced cell cycle arrest and apoptotic cells. Furthermore, we investigated the FAM111B-mediated molecular networks in LUAD cells. Identifying target genes regulated by passenger strands of miRNAs may aid in the discovery of diagnostic markers and therapeutic targets for LUAD.
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Affiliation(s)
- Yuya Tomioka
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Naohiko Seki
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan; (Y.G.); (N.K.)
| | - Takayuki Suetsugu
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Yoko Hagihara
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Hiroki Sanada
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Yusuke Goto
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan; (Y.G.); (N.K.)
| | - Naoko Kikkawa
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan; (Y.G.); (N.K.)
| | - Keiko Mizuno
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Kentaro Tanaka
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.T.); (T.S.); (Y.H.); (H.S.); (K.M.); (K.T.); (H.I.)
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Zhu Y, Koleilat MKI, Roszik J, Kwong MK, Wang Z, Maru DM, Kopetz S, Kwong LN. A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics. Cancers (Basel) 2024; 16:1886. [PMID: 38791964 PMCID: PMC11120226 DOI: 10.3390/cancers16101886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Mohamad Karim I. Koleilat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Man Kam Kwong
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Zhonglin Wang
- Social Science Research Institute, Duke University, Durham, NC 27708, USA;
| | - Dipen M. Maru
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Naicker D, Rhoda C, Sunda F, Arowolo A. Unravelling the Intricate Roles of FAM111A and FAM111B: From Protease-Mediated Cellular Processes to Disease Implications. Int J Mol Sci 2024; 25:2845. [PMID: 38474092 DOI: 10.3390/ijms25052845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Proteases are critical enzymes in cellular processes which regulate intricate events like cellular proliferation, differentiation and apoptosis. This review highlights the multifaceted roles of the serine proteases FAM111A and FAM111B, exploring their impact on cellular functions and diseases. FAM111A is implicated in DNA replication and replication fork protection, thereby maintaining genome integrity. Additionally, FAM111A functions as an antiviral factor against DNA and RNA viruses. Apart from being involved in DNA repair, FAM111B, a paralog of FAM111A, participates in cell cycle regulation and apoptosis. It influences the apoptotic pathway by upregulating anti-apoptotic proteins and modulating cell cycle-related proteins. Furthermore, FAM111B's association with nucleoporins suggests its involvement in nucleo-cytoplasmic trafficking and plays a role in maintaining normal telomere length. FAM111A and FAM111B also exhibit some interconnectedness and functional similarity despite their distinct roles in cellular processes and associated diseases resulting from their dysfunction. FAM111A and FAM111B dysregulation are linked to genetic disorders: Kenny-Caffey Syndrome type 2 and Gracile Bone Dysplasia for FAM111A and POIKTMP, respectively, and cancers. Therefore, the dysregulation of these proteases in diseases emphasizes their potential as diagnostic markers and therapeutic targets. Future research is essential to unravel the intricate mechanisms governing FAM111A and FAM111B and explore their therapeutic implications comprehensively.
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Affiliation(s)
- Danielle Naicker
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Falone Sunda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Afolake Arowolo
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town 7500, South Africa
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Wang H, Wang H, Chen J, Liu P, Xiao X. Overexpressed FAM111B degrades GSDMA to promote esophageal cancer tumorigenesis and cisplatin resistance. Cell Oncol (Dordr) 2024; 47:343-359. [PMID: 37672204 DOI: 10.1007/s13402-023-00871-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Chemotherapeutic agents such as cisplatin are commonly used in patients with clinically unresectable or recurrent esophageal cancer (ESCA). However, patients often develop resistance to cisplatin, which in turn leads to a poor prognosis. Studies have shown that FAM111B may be involved in the development of tumors as an oncogene or tumor suppressor gene. However, the pathological role and corresponding mechanism of FAM111B in ESCA are still unclear. METHODS The GEPIA web tool, ENCORI Pan-Cancer Analysis Platform and UALCAN-TCGA database were used to study the expression of FAM111B in ESCA. CCK-8, angiogenesis, Transwell and xenograft assays were applied to explore the biological function of FAM111B in ESCA. Western blot, RT-qPCR, and RNA-seq analyses were applied to study the FAM111B/GSDMA axis in the progression of ESCA cells. CCK-8 and xenograft assays were used to study the role of the FAM111B/GSDMA axis in determining the sensitivity of ESCA to cisplatin. RESULTS Our results demonstrated that FAM111B is highly expressed in ESCA tissues compared to normal tissues. We showed that FAM111B promotes the progression of ESCC cells by binding to GSDMA and that the trypsin protease domain is essential for the activity of FAM111B. Furthermore, we showed that the FAM111B/GSDMA axis regulates cisplatin sensitivity in ESCA. CONCLUSIONS Overall, we identified a novel FAM111B/GSDMA axis regulating ESCA tumorigenesis and chemosensitivity, at least in ESCC cells.
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Affiliation(s)
- Haiqin Wang
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Medical Research Center for Geriatric Syndrome, Changsha, Hunan, China
| | - Haohui Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiajing Chen
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Medical Research Center for Geriatric Syndrome, Changsha, Hunan, China
| | - Pian Liu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Cancer Center, Wuhan, Hubei, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China.
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Yang Y, Yan Z, Jiao Y, Yang W, Cui Q, Chen S. Family with sequence similarity 111 member B contributes to tumor growth and metastasis by mediating cell proliferation, invasion, and EMT via transforming acidic coiled-coil protein 3/PI3K/AKT signaling pathway in hepatocellular carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:409-420. [PMID: 37782700 DOI: 10.1002/tox.23965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/20/2023] [Accepted: 08/27/2023] [Indexed: 10/04/2023]
Abstract
As a complex systemic disease, primary liver cancer ranks third in death rate for solid tumors worldwide. Family with sequence similarity 111 member B (FAM111B), which was found to be aberrantly mutated in multiple cancers, is a candidate oncogene. We aimed to determine the function and mechanism of FAM111B in hepatocellular carcinoma (HCC). The expression of FAM111B was evaluated in HCC tissues, adjacent tissues, HCC cell lines. The impact of FAM111B on proliferation, invasion, apoptosis and EMT of HCC cells were detected by CCK-8, Transwell, flow cytometry and Western blot assays. The relationship between FAM111B and transforming acidic coiled-coil protein 3 (TACC3) was assessed by CoIP and Immunofluorescence (IF) staining assays. The effect of FAM111B on tumor growth was detected by using xenograft model of nude mice. The expression of FAM111B was upregulated in HCC tissues and cell lines, and the prognosis of HCC patients was worse in the high FAM111B expression group, and its expression level was associated with the TNM stage of HCC. FAM111B silencing inhibited HCC cell proliferation and invasion, EMT and induced apoptosis. Besides, TACC3 served as an interactor for FAM111B, which could enhance TACC3 expression, thus activing PI3K/AKT pathway. Rescue experiments revealed that elevated of TACC3 restored the inhibitory effect of FAM111B overexpression on the cell functions via PI3K/AKT pathway. In vivo, FAM111B inhibition hampered tumor growth and metastasis of HCC. This study highlighted a key player of FAM111B in modulating the malignant biological progression of HCC via TACC3/PI3K/AKT signaling pathway, displaying a potential therapeutic target for HCC.
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Affiliation(s)
- Yaobo Yang
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Zhaoyong Yan
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Yang Jiao
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Weihao Yang
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Qi Cui
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Sipan Chen
- Department of Interventional Radiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
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Li F, He HY, Fan ZH, Li CM, Gong Y, Wang XJ, Xiong HJ, Xie CM, Bie P. Silencing of FAM111B inhibited proliferation, migration and invasion of hepatoma cells through activating p53 pathway. Dig Liver Dis 2023; 55:1679-1689. [PMID: 37270349 DOI: 10.1016/j.dld.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND The function of Family with sequence similarity 111 member B (FAM111B) has been reported in multiple malignancies, but its involvement in occurrence and development of hepatocellular carcinoma (HCC) is still unclear. PURPOSE To investigate the role of FAM111B in HCC and explore the potential molecular mechanism. METHODS We examined the mRNA level of FAM111B via qPCR and protein level via immunohistochemistry in human HCC tissues. siRNA was used to construct a FAM111B-knockdown model in HCC cell lines. CCK-8, colony formation, transwell, and wound healing assays were performed to investigate the effect of FAM111B on proliferation, migration and invasion of HCC cell. Gene Set Enrichment Analysis, western blotting, and flow cytometry were carried out to find the related molecular mechanism. RESULTS Human HCC tumor tissues exhibited higher expression of FAM111B, and high FAM111B expression was associated with poor prognosis. Vitro assays demonstrated that knockdown of FAM111B greatly repressed proliferation, migration and invasion of HCC cells. Furthermore, silencing of FAM111B significantly resulted in cell cycle arrest at G0/G1 and downregulation of epithelial-mesenchymal transition (EMT)-related proteins MMP7 and MMP9 via activation of p53 pathway. CONCLUSION FAM111B played an essential role in promoting HCC development by regulation of p53 pathway.
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Affiliation(s)
- Feng Li
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, PR China
| | - Hong-Ye He
- Institute of Ultrasound Imaging & Department of Ultrasound, The Second Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ultrasound Molecular Imaging, Chongqing 400010, PR China
| | - Zhi-Hao Fan
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, PR China
| | - Chun-Ming Li
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Yi Gong
- Department of Hepatobiliary and Pancreatic Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, PR China
| | - Xiao-Jun Wang
- Department of Hepatobiliary and Pancreatic Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, PR China
| | - Hao-Jun Xiong
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, PR China.
| | - Chuan-Ming Xie
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, PR China.
| | - Ping Bie
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, PR China.
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Rios-Szwed DO, Alvarez V, Sanchez-Pulido L, Garcia-Wilson E, Jiang H, Bandau S, Lamond A, Alabert C. FAM111A regulates replication origin activation and cell fitness. Life Sci Alliance 2023; 6:e202302111. [PMID: 37793778 PMCID: PMC10551639 DOI: 10.26508/lsa.202302111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
FAM111A is a replisome-associated protein and dominant mutations within its trypsin-like peptidase domain are linked to severe human developmental syndrome, the Kenny-Caffey syndrome. However, FAM111A functions remain unclear. Here, we show that FAM111A facilitates efficient activation of DNA replication origins. Upon hydroxyurea treatment, FAM111A-depleted cells exhibit reduced single-stranded DNA formation and a better survival rate. Unrestrained expression of FAM111A WT and patient mutants causes accumulation of DNA damage and cell death, only when the peptidase domain remains intact. Unrestrained expression of FAM111A WT also causes increased single-stranded DNA formation that relies on S phase entry, FAM111A peptidase activity but not its binding to proliferating cell nuclear antigen. Altogether, these data unveil how FAM111A promotes DNA replication under normal conditions and becomes harmful in a disease context.
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Affiliation(s)
- Diana O Rios-Szwed
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vanesa Alvarez
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Luis Sanchez-Pulido
- https://ror.org/01nrxwf90 MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, UK
| | - Elisa Garcia-Wilson
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hao Jiang
- https://ror.org/03h2bxq36 MCDB, Quantitative Proteomics Laboratory, School of Life Sciences, University of Dundee, Dundee, UK
| | - Susanne Bandau
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Angus Lamond
- https://ror.org/03h2bxq36 MCDB, Quantitative Proteomics Laboratory, School of Life Sciences, University of Dundee, Dundee, UK
| | - Constance Alabert
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
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Huang N, Peng L, Yang J, Li J, Zhang S, Sun M. FAM111B Acts as an Oncogene in Bladder Cancer. Cancers (Basel) 2023; 15:5122. [PMID: 37958297 PMCID: PMC10648174 DOI: 10.3390/cancers15215122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Bladder cancer (BLCA) is a prevalent malignancy of the urinary system, associated with a high recurrence rate and poor prognosis. FAM111B, which encodes a protein containing a trypsin-like cysteine/serine peptidase domain, has been implicated in the progression of various human cancers; however, its involvement in BLCA remains unclear. In this study, we investigated the expression of FAM111B gene in tumor tissues compared to para-tumor tissues using immunohistochemistry and observed a significantly higher FAM111B gene expression in tumor tissues. Furthermore, analysis of clinical characteristics indicated that the increased FAM111B gene expression correlated with lymphatic metastasis and reduced overall survival. To investigate its functional role, we employed FAM111B-knockdown BLCA cell models and performed cell proliferation, wound-healing, transwell, and flow cytometry assays. The results showed that decreased FAM111B gene expression inhibited proliferation and migration but induced apoptosis in BLCA cells. In vivo experiments further validated that FAM111B knockdown suppressed tumor growth. Overall, our findings suggest that FAM111B acts as an oncogene in BLCA, playing a critical role in tumorigenesis, progression, and metastasis of BLCA. In conclusion, we have demonstrated a strong correlation between the expression of FAM111B gene and the development, progression, and metastasis of bladder cancer (BLCA). Thus, FAM111B is an oncogene associated with BLCA and holds promise as a molecular target for future treatment of this cancer.
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Affiliation(s)
- Ning Huang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Lei Peng
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Jiaping Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Jinqian Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Sheng Zhang
- Medical Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
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Morovat P, Morovat S, Hosseinpour M, Moslabeh FGZ, Kamali MJ, Samadani AA. Survival-based bioinformatics analysis to identify hub long non-coding RNAs along with lncRNA-miRNA-mRNA network for potential diagnosis/prognosis of thyroid cancer. J Cell Commun Signal 2023; 17:639-655. [PMID: 36149574 PMCID: PMC10409689 DOI: 10.1007/s12079-022-00697-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/07/2022] [Indexed: 11/26/2022] Open
Abstract
Thyroid cancer (TC) is the most common endocrine cancer, accounting for 1.7% of all cancer cases. It has been reported that the existing approach to diagnosing TC is problematic. Therefore, it is essential to develop molecular biomarkers to improve the accuracy of the diagnosis. This study aimed to screen hub lncRNAs in the ceRNA network (ceRNET) connected to TC formation and progression based on the overall survival rate. In this study, first, RNA-seq data from the GDC database were collected. A package called edgeR in R programming language was then used to obtain differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) in TC patients' samples compared to normal samples. Second, DEmRNAs were analyzed for their functional enrichment. Third, to identify RNAs associated with overall survival, the overall survival of these RNAs was analyzed using the Kaplan-Meier plotter database to create a survival associated with the ceRNA network (survival-related ceRNET). Next, the GeneMANIA plugin was used to construct a PPI network to better understand survival-related DEmRNA interactions. The survival ceRNET was then visualized with the Cytoscape software, and hub genes, including hub lncRNAs and hub mRNAs, were identified using the CytoHubba plugin. We found 45 DElncRNAs, 28 DEmiRNAs, and 723 DEmRNAs among thyroid tumor tissue and non-tumor tissue samples. According to KEGG, GO and DO analyses, 723 DEmRNAs were mainly enriched in cancer-related pathways. Importantly, the results found that ten DElncRNAs, four DEmiRNAs, and 68 DEmRNAs are associated with overall survival. In this account, the PPI network was constructed for 68 survival-related DEmRNAs, and ADAMTS9, DTX4, and CLDN10 were identified as hub genes. The ceRNET was created by combining six lncRNAs, 109 miRNAs, and 22 mRNAs related to survival using Cytoscape. in this network, ten hub RNAs were identified by the CytoHubba plugin, including mRNAs (CTXND1, XKRX, IGFBP2, ENTPD1, GALNT7, ADAMTS9) and lncRNAs (AC090673.1, AL162511.1, LINC02454, AL365259.1). This study suggests that three lncRNAs, including AL162511.1, AC090673.1, and AL365259.1, could be reliable diagnostic biomarkers for TC. The findings of this study provide a basis for future studies on the therapeutic potential of these lncRNAs.
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Affiliation(s)
- Pejman Morovat
- Department of Medical Biotechnology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Saman Morovat
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Milad Hosseinpour
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | | | - Mohammad Javad Kamali
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran.
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10
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Kliszczak M, Moralli D, Jankowska JD, Bryjka P, Subha Meem L, Goncalves T, Hester SS, Fischer R, Clynes D, Green CM. Loss of FAM111B protease mutated in hereditary fibrosing poikiloderma negatively regulates telomere length. Front Cell Dev Biol 2023; 11:1175069. [PMID: 37342232 PMCID: PMC10277729 DOI: 10.3389/fcell.2023.1175069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 06/22/2023] Open
Abstract
Hereditary fibrosing poikiloderma (HFP) is a rare human dominant negative disorder caused by mutations in the FAM111B gene that encodes a nuclear trypsin-like serine protease. HFP patients present with symptoms including skin abnormalities, tendon contractures, myopathy and lung fibrosis. We characterized the cellular roles of human FAM111B using U2OS and MCF7 cell lines and report here that the protease interacts with components of the nuclear pore complex. Loss of FAM111B expression resulted in abnormal nuclear shape and reduced telomeric DNA content suggesting that FAM111B protease is required for normal telomere length; we show that this function is independent of telomerase or recombination driven telomere extension. Even though FAM111B-deficient cells were proficient in DNA repair, they showed hallmarks of genomic instability such as increased levels of micronuclei and ultra-fine DNA bridges. When mutated as in HFP, FAM111B was more frequently localized to the nuclear envelope, suggesting that accumulation of the mutated protease at the nuclear periphery may drive the disease pathology.
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Affiliation(s)
- Maciej Kliszczak
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julia D. Jankowska
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paulina Bryjka
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lamia Subha Meem
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomas Goncalves
- Oncology Department, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Svenja S. Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Oxford, United Kingdom
| | - David Clynes
- Oncology Department, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Catherine M. Green
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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11
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Wang W, Gu Y, Ni H, Quan Q, Guo L. Silencing of FAM111B inhibits tumor growth and promotes apoptosis by decreasing AKT activity in ovarian cancer. Exp Biol Med (Maywood) 2023; 248:1043-1055. [PMID: 37095701 PMCID: PMC10581161 DOI: 10.1177/15353702231160326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 04/26/2023] Open
Abstract
Ovarian cancer is the most lethal gynecological tumor in women worldwide. FAM111B (family with sequence similarity 111 member B) is an oncoprotein associated with multiple cancers, but its biological functions in ovarian cancer remain elusive. In this study, FAM111B was overexpressed in ovarian cancer tissues and cell lines. Functional studies in vitro revealed that silencing of FAM111B inhibited ovarian cancer cell proliferation, invasion, and migration, as well as increased cell apoptosis. Furthermore, FAM111B silencing arrested the ovarian cancer cell cycle at the G1/S phase. Furthermore, western blot assays demonstrated that silencing of FAM111B resulted in downregulation of phospho-AKT (p-AKT) protein expression, as well as upregulation of p53 and caspase-1 protein expression. The xenograft animal model of ovarian cancer demonstrated that FAM111B silencing inhibited tumor growth, enhanced cell apoptosis, and inhibited Ki-67 and proliferating cell nuclear antigen (PCNA) protein expression in vivo. Conversely, the overexpression of FAM111B exhibited opposite effects on the ovarian cancer xenograft. It was previously established that inactivating AKT inhibited ovarian cancer progression. This study found that silencing of FAM111B inhibits tumor growth and promotes apoptosis by decreasing AKT activity in ovarian cancer. Caspase-1 and p53 signaling also influenced the function of FAM111B in SKOV3 cells. Collectively, our results demonstrate that silencing of FAM111B is a potential therapeutic strategy against ovarian cancer.
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Affiliation(s)
- Wei Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
- Department of Pathology, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, China
| | - Yun Gu
- Department of Pathology, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Hao Ni
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Qiuying Quan
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Lingchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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12
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Wei F, Yu G, Si C, Chao T, Xiong H, Zhang L. High FAM111B expression predicts aggressive clinicopathologic features and poor prognosis in ovarian cancer. Transl Oncol 2023; 32:101659. [PMID: 36963205 PMCID: PMC10060368 DOI: 10.1016/j.tranon.2023.101659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/22/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUNDS Ovarian cancer (OC) is the second most common gynecological tumor with the highest mortality rate worldwide. High FAM111B expression has been reported as a predictor of poor prognosis in other cancers, but its correlation with OC has not been reported. METHODS Immunohistochemistry of tissue microarrays was performed to detect FAM111B expression levels in 141 OC patient tissues. The prognostic value of FAM111B was determined by Kaplan-Meier survival analysis, and correlations between FAM111B expression and clinicopathologic features were investigated by the Clu-square test. The significance of FAM111B expression was verified bioinformatically using the Gene Expression Omnibus database. Protein-protein interaction were performed to explore downstream mechanisms of FAM111B in OC. RESULTS Among 141 OC patients, FAM111B was positively expressed in 87.23%, 58.16%, and 87.94%; and highly expressed in 8.51%, 17.02%, and 19.86%, as evaluated by cytoplasmic, nuclear, and combined cytoplasmic/nuclear staining. FAM111B expression was positively correlated with the expression of tumor protein markers KI67, EGFR, and PDL-1. Patients with high FAM111B expression had aggressive clinicopathologic features and shorter overall survival (P value 0.0428, 0.0050, 0.0029) and progression-free survival (P value 0.0251, 0.012, 0.0596) compared to the low FAM111B expression group for cytoplasmic, nuclear, and combined cytoplasmic/nuclear groups, respectively. These results were verified using patient data from the Gene Expression Omnibus. Seventeen genes co-expressed with FAM111B were primarily involved in "negative regulation of histone modification", "hippo signaling" and "inner ear receptor cell differentiation". CONCLUSIONS High FAM111B expression may serve as a novel prognostic predictor and molecular therapeutic target for OC.
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Affiliation(s)
- Fang Wei
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guoyu Yu
- Department of Oncology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China
| | - Chaozeng Si
- Information Center, China-Japan Friendship Hospital, Beijing, China
| | - Tengfei Chao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lihong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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13
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Kin R, Hoshi D, Fujita H, Kosaka T, Takamura H, Kiyokawa E. Prognostic significance of p16, p21, and Ki67 expression at the invasive front of colorectal cancers. Pathol Int 2023; 73:81-90. [PMID: 36484761 DOI: 10.1111/pin.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Cancer cells at the invasive front are believed to be responsible for invasion/metastasis. This has led to examining various morphological features and protein expressions at the invasive front. However, accurate assessment of the pathological section requires long-time training, and inter-observer disagreement is problematic. Immunohistochemistry and digital imaging analysis may mitigate these problems; however, the choice of which proteins to stain and the best analysis method remains controversial. We used the "go-or-grow" hypothesis to select markers with the greatest prognostic relevance. Importantly, nonproliferating cells can migrate. We used Ki67 as a proliferation marker, with p16 and p21 designating nonproliferating cells. We established a semi-automated quantification workflow to study protein expression in serial pathological sections. A total of 51 patients with completely resected colorectal cancer (stages I-IV) were analyzed, and 44 patients were followed up. Patients with cancer cells with p16-high/p21-low or p21-low/Ki67-low at the deepest invasive front demonstrated a significantly worse prognosis than those who did not display these characteristics. These results suggest that the nonproliferating cancer cells at the invasion front possess invasion/metastatic property with heterogeneity of senescence.
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Affiliation(s)
- Ryosuke Kin
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan
| | - Daisuke Hoshi
- Department of Oncologic Pathology, Kanazawa Medical University, Ishikawa, Japan
| | - Hideto Fujita
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan
| | - Takeo Kosaka
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan.,Department of Surgery, Houju Memorial Hospital, Ishikawa, Japan
| | | | - Etsuko Kiyokawa
- Department of Oncologic Pathology, Kanazawa Medical University, Ishikawa, Japan
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14
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Hong K, Cen K, Chen Q, Dai Y, Mai Y, Guo Y. Identification and validation of a novel senescence-related biomarker for thyroid cancer to predict the prognosis and immunotherapy. Front Immunol 2023; 14:1128390. [PMID: 36761753 PMCID: PMC9902917 DOI: 10.3389/fimmu.2023.1128390] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Cellular senescence is a hallmark of tumors and has potential for cancer therapy. Cellular senescence of tumor cells plays a role in tumor progression, and patient prognosis is related to the tumor microenvironment (TME). This study aimed to explore the predictive value of senescence-related genes in thyroid cancer (THCA) and their relationship with the TME. Methods Senescence-related genes were identified from the Molecular Signatures Database and used to conduct consensus clustering across TCGA-THCA. Differentially expressed genes (DEGs) were identified between the clusters used to perform multivariate Cox regression and least absolute shrinkage and selection operator regression (LASSO) analyses to construct a senescence-related signature. TCGA dataset was randomly divided into training and test datasets to verify the prognostic ability of the signature. Subsequently, the immune cell infiltration pattern, immunotherapy response, and drug sensitivity of the two subtypes were analyzed. Finally, the expression of signature genes was detected across TCGA-THCA and GSE33630 datasets, and further validated by RT-qPCR. Results Three senescence clusters were identified based on the expression of 432 senescence-related genes. Then, 23 prognostic DEGs were identified in TCGA dataset. The signature, composed of six genes, showed a significant relationship with survival, immune cell infiltration, clinical characteristics, immune checkpoints, immunotherapy response, and drug sensitivity. Low-risk THCA shows a better prognosis and higher immunotherapy response than high-risk THCA. A nomogram with perfect stability constructed using signature and clinical characteristics can predict the survival of each patient. The validation part demonstrated that ADAMTSL4, DOCK6, FAM111B, and SEMA6B were expressed at higher levels in the tumor tissue, whereas lower expression of MRPS10 and PSMB7 was observed. Discussion In conclusion, the senescence-related signature is a promising biomarker for predicting the outcome of THCA and has the potential to guide immunotherapy.
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Affiliation(s)
- Kai Hong
- Department of Thyroid and Breast Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China,Department of Thyroid and Breast Surgery, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China
| | - Kenan Cen
- Department of Geriatrics Medicine, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Qiaoqiao Chen
- Reproductive Medicine Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Dai
- Department of Geriatrics Medicine, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Yifeng Mai
- Department of Geriatrics Medicine, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China,*Correspondence: Yangyang Guo, ; Yifeng Mai,
| | - Yangyang Guo
- Department of Thyroid and Breast Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China,Department of Thyroid and Breast Surgery, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China,*Correspondence: Yangyang Guo, ; Yifeng Mai,
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15
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Hoeger PH, Koehler LM, Reipschlaeger M, Mercier S. Hereditary fibrosing poikiloderma (POIKTMP syndrome) report of a new mutation and review of the literature. Pediatr Dermatol 2023; 40:182-187. [PMID: 36102338 DOI: 10.1111/pde.15133] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023]
Abstract
Hereditary fibrosing poikiloderma with tendon contractures, myopathy, and pulmonary fibrosis (POIKTMP) is a genodermatosis with autosomal dominant inheritance caused by mutations in FAM111B. We report another case with a new pathogenic variant and analyze all previously published 34 cases with a focus on sequence of clinical presentation and genotype-phenotype correlation. POIKTMP is characterized by marked age-dependent clinical expressivity. FAM111B encodes a catalytic nuclear protein, expressed in many tissues, which contributes to impaired DNA repair affecting multiple systems. Specific inhibition of catalytic activity might be a future strategy to halt progression of this otherwise untreatable disease. Given the relentless progression of the disease, it would make sense to start such treatment as early as possible. In order to achieve this objective, children with suspected POIKTMP should therefore undergo early imaging of all relevant organ systems.
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Affiliation(s)
- Peter H Hoeger
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany.,Department of Pediatric Dermatology, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Lisa M Koehler
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany.,Department of Pediatric Dermatology, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Maria Reipschlaeger
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence des Maladies Neuromusculaires AOC, Filnemus, Euro-NMD, Nantes, France.,Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
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16
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Rhoda C, Sunda F, Kidzeru E, Khumalo NP, Arowolo A. FAM111B dysregulation promotes malignancy in fibrosarcoma and POIKTMP and a low-cost method for its mutation screening. Cancer Treat Res Commun 2023; 34:100679. [PMID: 36610347 DOI: 10.1016/j.ctarc.2022.100679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/05/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Mutations in the uncharacterised human FAM111B gene are associated with POIKTMP, a rare multi-organ fibrosing disease. Recent studies also reported the overexpression of FAM111B in specific cancers. Moreover, FAM111B mutation screening may prove expensive in under-resourced facilities. Therefore, this study investigated its cellular function and dysfunction and described an inexpensive mutation screening method. MATERIALS AND METHODS FAM111B expression was assessed in silico and validated in vitro in cell lines and primary skin fibroblasts from a South African POIKTMP-patient with the heterozygous FAM111B gene mutation: NM_198947.4: c.1861T>G (p. Tyr621Asp or Y621D) by qPCR and western blot. The cellular function of FAM111B was studied in HT1080 using various cell-based functional assays, and the Y621D mutation was genotyped by PCR-RFLP. RESULTS Expression studies showed upregulated FAM111B mRNA and protein in the cancer cells. High FAM111B expression with robust nuclear localization occurred in HT1080. Additionally, expression data and cell-based assays indicated that FAM111B led to the upregulation of cell migration, decreased cell apoptosis, and modulatory effects on cell proliferation. Y621D mutation showed similar effects on cell migration but minimal impact on cell apoptosis. FAM111B mRNA and protein expression were markedly downregulated (p ≤ 0.05) in the POIKTMP-patient's fibroblasts. The PCR-RFLP method successfully genotyped Y621D gene mutation. DISCUSSION FAM111B is a cancer-associated nuclear protein: Its modulation by mutations or overexpression may contribute to the malignancy of cancers and POIKTMP/fibrosis and poor clinical outcomes and represents a viable prognostic marker or therapeutic target. Furthermore, the PCR-RFLP method could prove a valuable tool for FAM111B mutation validation or screening in resource-constrained laboratories.
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Affiliation(s)
- Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Falone Sunda
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Elvis Kidzeru
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
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17
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Wu H, Liang C. Pan-Cancer Analysis of the Tumorigenic Effect and Prognostic Diagnostic Value of FAM111B in Human Carcinomas. Int J Gen Med 2023; 16:1845-1865. [PMID: 37213474 PMCID: PMC10199687 DOI: 10.2147/ijgm.s409690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction FAM111B (FAM111 trypsin-like peptidase B) gene mutations have been linked to a hereditary fibrosing poikiloderma disorder known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). Overexpression of FAM111B has been associated with an increased risk of certain cancers with a poor prognosis, although the relationship between FAM111B and other tumors is still unclear, and the molecular mechanism of its action is not fully understood. Methods We investigated the biological functions of FAM111B in 33 solid tumors using multi-omics data. We further recruited 109 gastric cancer (GC) patients for a clinical cohort study to confirm the effect of FAM111B on early tumor recurrence. Furthermore, we assessed the role of FAM111B in GC cell proliferation and migration via EdU incorporation, CCK8 and transwell assays in vitro. Results We found that FAM111B can enhance oncogenesis and progression in multiple tumor types. The clinical cohort of GC showed that upregulation of FAM111B is associated with early recurrence of GC, and knockdown of the FAM111B gene can inhibit the proliferation and migration of GC cells. Gene enrichment analysis indicates that FAM111B promotes cancer through immune system process, chromosome instability, DNA repair, and apoptosis regulation. Mechanistically, FAM111B appears to promote the growth cycle of malignant tumor cells while inhibiting apoptosis. Conclusion FAM111B may serve as a potential pan-cancer biomarker for predicting the prognosis and survival of malignant tumor patients. Our study elucidates the role of FAM111B in the occurrence and development of various cancers, and highlights the need for future research on FAM111B in cancers.
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Affiliation(s)
- Hengmiao Wu
- Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315000, People’s Republic of China
| | - Chao Liang
- Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315000, People’s Republic of China
- Correspondence: Chao Liang, Department of General Surgery, the Affiliated Lihuili Hospital, Ningbo University, 57 Xingning Road, Ningbo, 315000, People’s Republic of China, Tel +86-574-87018607, Email
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18
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Welter AL, Machida YJ. Functions and evolution of FAM111 serine proteases. Front Mol Biosci 2022; 9:1081166. [PMID: 36589246 PMCID: PMC9798293 DOI: 10.3389/fmolb.2022.1081166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Proteolysis plays fundamental and regulatory roles in diverse cellular processes. The serine protease FAM111A (FAM111 trypsin-like peptidase A) emerged recently as a protease involved in two seemingly distinct processes: DNA replication and antiviral defense. FAM111A localizes to nascent DNA and plays a role at the DNA replication fork. At the fork, FAM111A is hypothesized to promote DNA replication at DNA-protein crosslinks (DPCs) and protein obstacles. On the other hand, FAM111A has also been identified as a host restriction factor for mutants of SV40 and orthopoxviruses. FAM111A also has a paralog, FAM111B, a serine protease with unknown cellular functions. Furthermore, heterozygous missense mutations in FAM111A and FAM111B cause distinct genetic disorders. In this review, we discuss possible models that could explain how FAM111A can function as a protease in both DNA replication and antiviral defense. We also review the consequences of FAM111A and FAM111B mutations and explore possible mechanisms underlying the diseases. Additionally, we propose a possible explanation for what drove the evolution of FAM111 proteins and discuss why some species have two FAM111 proteases. Altogether, studies of FAM111 proteases in DNA repair, antiviral defense, and genetic diseases will help us elucidate their functions and the regulatory mechanisms.
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Affiliation(s)
- Allison L. Welter
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Yuichi J. Machida
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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19
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Gong Q, Dong Q, Zhong B, Zhang T, Cao D, Zhang Y, Ma D, Cai X, Li Z. Clinicopathological features, prognostic significance, and associated tumor cell functions of family with sequence similarity 111 member B in pancreatic adenocarcinoma. J Clin Lab Anal 2022; 36:e24784. [DOI: 10.1002/jcla.24784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/31/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Qi Gong
- Wuhan University of Science and Technology School of Medicine Wuhan China
| | - QingTai Dong
- The First School of Clinical Medicine Southern Medical University Guangzhou China
| | - Bin Zhong
- The First School of Clinical Medicine Southern Medical University Guangzhou China
| | - Tao Zhang
- Wuhan University of Science and Technology School of Medicine Wuhan China
| | - Ding Cao
- Department of General Surgery General Hospital of Central Theatre Command Wuhan China
| | - Yi Zhang
- Department of General Surgery General Hospital of Central Theatre Command Wuhan China
| | - Dandan Ma
- Department of General Surgery General Hospital of Central Theatre Command Wuhan China
| | - Xun Cai
- Department of General Surgery General Hospital of Central Theatre Command Wuhan China
| | - ZhongHu Li
- Department of General Surgery General Hospital of Central Theatre Command Wuhan China
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20
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Gonzalez-Salinas F, Martinez-Amador C, Trevino V. Characterizing genes associated with cancer using the CRISPR/Cas9 system: A systematic review of genes and methodological approaches. Gene 2022; 833:146595. [PMID: 35598687 DOI: 10.1016/j.gene.2022.146595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022]
Abstract
The CRISPR/Cas9 system enables a versatile set of genomes editing and genetic-based disease modeling tools due to its high specificity, efficiency, and accessible design and implementation. In cancer, the CRISPR/Cas9 system has been used to characterize genes and explore different mechanisms implicated in tumorigenesis. Different experimental strategies have been proposed in recent years, showing dependency on various intrinsic factors such as cancer type, gene function, mutation type, and technical approaches such as cell line, Cas9 expression, and transfection options. However, the successful methodological approaches, genes, and other experimental factors have not been analyzed. We, therefore, initially considered more than 1,300 research articles related to CRISPR/Cas9 in cancer to finally examine more than 400 full-text research publications. We summarize findings regarding target genes, RNA guide designs, cloning, Cas9 delivery systems, cell enrichment, and experimental validations. This analysis provides valuable information and guidance for future cancer gene validation experiments.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Claudia Martinez-Amador
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico; Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada avenue 2501, Monterrey, Nuevo Leon 64849, México.
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21
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Zhu X, Xue C, Kang X, Jia X, Wang L, Younis MH, Liu D, Huo N, Han Y, Chen Z, Fu J, Zhou C, Yao X, Du Y, Cai W, Kang L, Lyu Z. DNMT3B-mediated FAM111B methylation promotes papillary thyroid tumor glycolysis, growth and metastasis. Int J Biol Sci 2022; 18:4372-4387. [PMID: 35864964 PMCID: PMC9295055 DOI: 10.7150/ijbs.72397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/13/2022] [Indexed: 11/15/2022] Open
Abstract
Over the past decades, the incidence of thyroid cancer (TC) rapidly increased all over the world, with the papillary thyroid cancer (PTC) accounting for the vast majority of TC cases. It is crucial to investigate novel diagnostic and therapeutic targets for PTC and explore more detailed molecular mechanisms in the carcinogenesis and progression of PTC. Based on the TCGA and GEO databases, FAM111B is downregulated in PTC tissues and predicts better prognosis in PTC patients. FAM111B suppresses the growth, migration, invasion and glycolysis of PTC both in vitro and in vivo. Furthermore, estrogen inhibits FAM111B expression by DNMT3B methylation via enhancing the recruitment of DNMT3B to FAM111B promoter. DNMT3B-mediated FAM111B methylation accelerates the growth, migration, invasion and glycolysis of PTC cells. In clinical TC patient specimens, the expression of FAM111B is inversely correlated with the expressions of DNMT3B and the glycolytic gene PGK1. Besides, the expression of FAM111B is inversely correlated while DNMT3B is positively correlated with glucose uptake in PTC patients. Our work established E2/DNMT3B/FAM111B as a crucial axis in regulating the growth and progression of PTC. Suppression of DNMT3B or promotion of FAM111B will be potential promising strategies in the estrogen induced PTC.
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Affiliation(s)
- Xiang Zhu
- Department of Endocrinology, the First Medical Center of PLA General Hospital, Beijing, China.,Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Chunyuan Xue
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaofeng Kang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaomeng Jia
- Department of Endocrinology, the First Medical Center of PLA General Hospital, Beijing, China
| | - Lin Wang
- Department of Endocrinology, the First Medical Center of PLA General Hospital, Beijing, China
| | - Muhsin H Younis
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Donghui Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Nan Huo
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yuchen Han
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Zhao Chen
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, China
| | - Jing Fu
- Department of Pathology, Beijing Haidian Hospital, Beijing, China
| | - Chunyu Zhou
- Department of Pathology, Beijing Haidian Hospital, Beijing, China
| | - Xiaoxiang Yao
- Department of Pathology, Beijing Haidian Hospital, Beijing, China
| | - Yimeng Du
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Weibo Cai
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, China
| | - Zhaohui Lyu
- Department of Endocrinology, the First Medical Center of PLA General Hospital, Beijing, China
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22
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Arowolo A, Malebana M, Sunda F, Rhoda C. Proposed Cellular Function of the Human FAM111B Protein and Dysregulation in Fibrosis and Cancer. Front Oncol 2022; 12:932167. [PMID: 35860584 PMCID: PMC9293052 DOI: 10.3389/fonc.2022.932167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
FAM111B gene mutations are associated with a hereditary fibrosing poikiloderma known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). In addition, the overexpression of FAM111B has been associated with cancer progression and poor prognosis. This review inferred the molecular function of this gene's protein product and mutational dysfunction in fibrosis and cancer based on recent findings from studies on this gene. In conclusion, FAM111B represents an uncharacterized protease involved in DNA repair, cell cycle regulation, and apoptosis. The dysregulation of this protein ultimately leads to fibrotic diseases like POIKTMP and cancers via the disruption of these cellular processes by the mutation of the FAM111B gene. Hence, it should be studied in the context of these diseases as a possible therapeutic target.
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Affiliation(s)
- Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Moses Malebana
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Falone Sunda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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23
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Li W, Feng SS, Wu H, Deng J, Zhou WY, Jia MX, Shi Y, Ma L, Zeng XX, Zuberi Z, Fu D, Liu X, Chen Z. Comprehensive Analysis of CDK1-Associated ceRNA Network Revealing the Key Pathways LINC00460/LINC00525-Hsa-Mir-338-FAM111/ZWINT as Prognostic Biomarkers in Lung Adenocarcinoma Combined with Experiments. Cells 2022; 11:cells11071220. [PMID: 35406786 PMCID: PMC8997540 DOI: 10.3390/cells11071220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/20/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer deaths worldwide, and effective biomarkers are still lacking for early detection and prognosis prediction. Here, based on gene expression profiles of LUAD patients from The Cancer Genome Atlas (TCGA), 806 long non-coding RNAs (lncRNAs), 122 microRNAs (miRNAs) and 1269 mRNAs associated with CDK1 were identified. The regulatory axis of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT was determined according to the correlation between gene expression and patient prognosis. The abnormal up-regulation of FAM111B/ZWINT in LUAD was related to hypomethylation. Furthermore, immune infiltration analysis suggested FAM111B/ZWINT could affect the development and prognosis of cancer by regulating the LUAD immune microenvironment. EMT feature analysis suggested that FAM111B/ZWINT promoted tumor spread through the EMT process. Functional analysis showed FAM111B/ZWINT was involved in cell cycle events such as DNA replication and chromosome separation. We analyzed the HERB and GSCALite databases to identify potential target medicines that may play a role in the treatment of LUAD. Finally, the expression of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT axis was verified in LUAD cells by RT-qPCR, and these results were consistent with bioinformatics analysis. Overall, we constructed a CDK1-related ceRNA network and revealed the LINC00460/LINC00525-hsa-mir-338-FAM111/ZWINT pathways as potential diagnostic biomarkers or therapeutic targets of LUAD.
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Affiliation(s)
- Wen Li
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Shan-Shan Feng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Hao Wu
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Jing Deng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Wang-Yan Zhou
- Department of Medical Record, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang 421001, China;
| | - Ming-Xi Jia
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Yi Shi
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Liang Ma
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Xiao-Xi Zeng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Zavuga Zuberi
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam P.O. Box 2958, Tanzania;
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China;
| | - Xiang Liu
- Department of Thoracic Surgery, Hengyang Medical School, The Second Affiliated Hospital, University of South China, Hengyang 421001, China
- Correspondence: (X.L.); (Z.C.); Tel.: +86-0734-889-9990 (X.L.); +86-158-6971-6968 (Z.C.)
| | - Zhu Chen
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
- Correspondence: (X.L.); (Z.C.); Tel.: +86-0734-889-9990 (X.L.); +86-158-6971-6968 (Z.C.)
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24
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Henriques-Pons A, Beghini DG, Silva VDS, Iwao Horita S, da Silva FAB. Pulmonary Mesenchymal Stem Cells in Mild Cases of COVID-19 Are Dedicated to Proliferation; In Severe Cases, They Control Inflammation, Make Cell Dispersion, and Tissue Regeneration. Front Immunol 2022; 12:780900. [PMID: 35095855 PMCID: PMC8793136 DOI: 10.3389/fimmu.2021.780900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent adult stem cells present in virtually all tissues; they have potent self-renewal capacity and differentiate into multiple cell types. For many reasons, these cells are a promising therapeutic alternative to treat patients with severe COVID-19 and pulmonary post-COVID sequelae. These cells are not only essential for tissue regeneration; they can also alter the pulmonary environment through the paracrine secretion of several mediators. They can control or promote inflammation, induce other stem cells differentiation, restrain the virus load, and much more. In this work, we performed single-cell RNA-seq data analysis of MSCs in bronchoalveolar lavage samples from control individuals and COVID-19 patients with mild and severe clinical conditions. When we compared samples from mild cases with control individuals, most genes transcriptionally upregulated in COVID-19 were involved in cell proliferation. However, a new set of genes with distinct biological functions was upregulated when we compared severely affected with mild COVID-19 patients. In this analysis, the cells upregulated genes related to cell dispersion/migration and induced the γ-activated sequence (GAS) genes, probably triggered by IFNGR1 and IFNGR2. Then, IRF-1 was upregulated, one of the GAS target genes, leading to the interferon-stimulated response (ISR) and the overexpression of many signature target genes. The MSCs also upregulated genes involved in the mesenchymal-epithelial transition, virus control, cell chemotaxis, and used the cytoplasmic RNA danger sensors RIG-1, MDA5, and PKR. In a non-comparative analysis, we observed that MSCs from severe cases do not express many NF-κB upstream receptors, such as Toll-like (TLRs) TLR-3, -7, and -8; tumor necrosis factor (TNFR1 or TNFR2), RANK, CD40, and IL-1R1. Indeed, many NF-κB inhibitors were upregulated, including PPP2CB, OPTN, NFKBIA, and FHL2, suggesting that MSCs do not play a role in the "cytokine storm" observed. Therefore, lung MSCs in COVID-19 sense immune danger and act protectively in concert with the pulmonary environment, confirming their therapeutic potential in cell-based therapy for COVID-19. The transcription of MSCs senescence markers is discussed.
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Affiliation(s)
- Andrea Henriques-Pons
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
| | - Daniela Gois Beghini
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
| | | | - Samuel Iwao Horita
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
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25
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Arowolo A, Rhoda C, Khumalo N. Mutations within the putative protease domain of the human FAM111B gene may predict disease severity and poor prognosis: A review of POIKTMP cases. Exp Dermatol 2022; 31:648-654. [PMID: 35122327 PMCID: PMC9344908 DOI: 10.1111/exd.14537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/22/2022] [Accepted: 02/01/2022] [Indexed: 11/27/2022]
Abstract
Mutations in the human FAM111B gene are associated with a rare, hereditary multi‐systemic fibrosing disease, POIKTMP. To date, there are ten POIKTMP‐associated FAM111B gene mutations reported in thirty‐six patients from five families globally. To investigate the clinical significance of these mutations, we summarized individual cases by clinical features and position of the reported FAM111B gene mutations as those within and outside the putative protease domain (MWPPD and MOPPD respectively). MWPPD cases had more clinical manifestations than MOPPD (25 versus 18). Although the most common clinical features of poikiloderma, alopecia and hypohidrosis overall occurred in 94%, 86% and 75% of all cases with no significant differences between the MOPPD and MWPPD group, less common features included life‐threatening (pulmonary fibrosis 47% vs. 13%; liver abnormalities specifically cirrhosis 26% vs. 7%) and physically disabling conditions (myopathy 53% vs. 20%; tendon contracture 55% vs. 7%) were more common in MWPPD cases. Similarly, the only 2 cases of POIKTMP with fatal pancreatic cancers were both only in the MWPPD group. This review thus suggests that mutations within the putative protease domain of the FAM111B protein are associated with a broader range of clinical features and may predict increased POIKTMP severity and a poorer prognosis.
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Affiliation(s)
- Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nonhlanhla Khumalo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
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26
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Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation. TOXICS 2021; 9:toxics9120338. [PMID: 34941772 PMCID: PMC8708250 DOI: 10.3390/toxics9120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023]
Abstract
Exposure to ambient air pollution during pregnancy has been associated with an increased risk of preeclampsia (PE). Some suggested mechanisms behind this association are changes in placental DNA methylation and gene expression. The objective of this study was to identify how early pregnancy exposure to ambient nitrogen oxides (NOx) among PE cases and normotensive controls influence DNA methylation (EPIC array) and gene expression (RNA-seq). The study included placentas from 111 women (29 PE cases/82 controls) in Scania, Sweden. First-trimester NOx exposure was assessed at the participants’ residence using a dispersion model and categorized via median split into high or low NOx. Placental gestational epigenetic age was derived from the DNA methylation data. We identified six differentially methylated positions (DMPs, q < 0.05) comparing controls with low NOx vs. cases with high NOx and 14 DMPs comparing cases and controls with high NOx. Placentas with female fetuses showed more DMPs (N = 309) than male-derived placentas (N = 1). Placentas from PE cases with high NOx demonstrated gestational age deceleration compared to controls with low NOx (p = 0.034). No differentially expressed genes (DEGs, q < 0.05) were found. In conclusion, early pregnancy exposure to NOx affected placental DNA methylation in PE, resulting in placental immaturity and showing sexual dimorphism.
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27
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Wu C, Huang ZH, Meng ZQ, Fan XT, Lu S, Tan YY, You LM, Huang JQ, Stalin A, Ye PZ, Wu ZS, Zhang JY, Liu XK, Zhou W, Zhang XM, Wu JR. A network pharmacology approach to reveal the pharmacological targets and biological mechanism of compound kushen injection for treating pancreatic cancer based on WGCNA and in vitro experiment validation. Chin Med 2021; 16:121. [PMID: 34809653 PMCID: PMC8607619 DOI: 10.1186/s13020-021-00534-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Compound kushen injection (CKI), a Chinese patent drug, is widely used in the treatment of various cancers, especially neoplasms of the digestive system. However, the underlying mechanism of CKI in pancreatic cancer (PC) treatment has not been totally elucidated. METHODS Here, to overcome the limitation of conventional network pharmacology methods with a weak combination with clinical information, this study proposes a network pharmacology approach of integrated bioinformatics that applies a weighted gene co-expression network analysis (WGCNA) to conventional network pharmacology, and then integrates molecular docking technology and biological experiments to verify the results of this network pharmacology analysis. RESULTS The WGCNA analysis revealed 2 gene modules closely associated with classification, staging and survival status of PC. Further CytoHubba analysis revealed 10 hub genes (NCAPG, BUB1, CDK1, TPX2, DLGAP5, INAVA, MST1R, TMPRSS4, TMEM92 and SFN) associated with the development of PC, and survival analysis found 5 genes (TSPOAP1, ADGRG6, GPR87, FAM111B and MMP28) associated with the prognosis and survival of PC. By integrating these results into the conventional network pharmacology study of CKI treating PC, we found that the mechanism of CKI for PC treatment was related to cell cycle, JAK-STAT, ErbB, PI3K-Akt and mTOR signalling pathways. Finally, we found that CDK1, JAK1, EGFR, MAPK1 and MAPK3 served as core genes regulated by CKI in PC treatment, and were further verified by molecular docking, cell proliferation assay, RT-qPCR and western blot analysis. CONCLUSIONS Overall, this study suggests that the optimized network pharmacology approach is suitable to explore the molecular mechanism of CKI in the treatment of PC, which provides a reference for further investigating biomarkers for diagnosis and prognosis of PC and even the clinical rational application of CKI.
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Affiliation(s)
- Chao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhi-Hong Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zi-Qi Meng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xiao-Tian Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Shan Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Ying-Ying Tan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Lei-Ming You
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jia-Qi Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Antony Stalin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, 311300, China
| | - Pei-Zhi Ye
- National Cancer Center/National Clinical Research Center for Cancer/Chinese Medicine Department of the Caner Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhi-Shan Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jing-Yuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xin-Kui Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Wei Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiao-Meng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jia-Rui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
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28
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Supervised learning based on tumor imaging and biopsy transcriptomics predicts response of hepatocellular carcinoma to transarterial chemoembolization. Cell Rep Med 2021; 2:100444. [PMID: 34841291 PMCID: PMC8606904 DOI: 10.1016/j.xcrm.2021.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/03/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022]
Abstract
Although transarterial chemoembolization (TACE) is the most widely used treatment for intermediate-stage, unresectable hepatocellular carcinoma (HCC), it is only effective in a subset of patients. In this study, we combine clinical, radiological, and genomics data in supervised machine-learning models toward the development of a clinically applicable predictive classifier of response to TACE in HCC patients. Our study consists of a discovery cohort of 33 tumors through which we identify predictive biomarkers, which are confirmed in a validation cohort. We find that radiological assessment of tumor area and several transcriptomic signatures, primarily the expression of FAM111B and HPRT1, are most predictive of response to TACE. Logistic regression decision support models consisting of tumor area and RNA-seq gene expression estimates for FAM111B and HPRT1 yield a predictive accuracy of ∼90%. Reverse transcription droplet digital PCR (RT-ddPCR) confirms these genes in combination with tumor area as a predictive classifier for response to TACE. Tumor imaging and transcriptomics enables patient selection for good response to TACE PRETACE is a LR model based on tumor area and expression of FAM111B and HPRT1 PRETACE predicts response to TACE with ∼90% accuracy
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29
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Li W, Hu S, Han Z, Jiang X. YY1-Induced Transcriptional Activation of FAM111B Contributes to the Malignancy of Breast Cancer. Clin Breast Cancer 2021; 22:e417-e425. [PMID: 34802969 DOI: 10.1016/j.clbc.2021.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Family with sequence similarity 111 member B (FAM111B) is an oncoprotein associated with multiple malignancies. We investigated the potential mechanisms of FAM111B in breast cancer. PATIENTS AND METHODS We tested the expression of FAM111B in breast cancer tissues and the survival rate of breast cancer patients with high or low level of FAM111B through TCGA data. The expression of FAM111B in breast cancer tissues and adjacent tissues was detected using western blotting. Then we used siRNA to construct a low expression model of FAM111B in SKBR3 and MDA-MB-468. EdU, CCK-8, wound healing, and transwell assays were performed to monitor the proliferation, migration, and invasion of breast cancer cells. Western blotting was used to detect the expression of EMT-related indicators. Chromatin Immunoprecipitation (ChIP) and qPCR were used to evaluate the regulatory effect of Yin Yang 1 (YY1) on FAM111B. RESULTS The expression of FAM111B in breast cancer tissues was higher than that in normal tissues. Patients who had high FAM111B expression had a worse prognosis. Knockdown of FAM111B inhibited the proliferation, migration, and invasion of breast cancer cells. Knockdown of FAM111B resulted in increased expression of EMT-related protein E-cadherin and decreased expression of N-cadherin and Vimentin. ChIP-qPCR analysis demonstrated that YY1 could bind to the promoter of FAM111B gene and strengthen its transcription activity. CONCLUSION YY1-induced transcriptional activation of FAM111B accelerated the progression of breast cancer.
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Affiliation(s)
- Wei Li
- Department of General surgery, Inner Mongolia Baogang Hospital, Inner Mongolia, P.R. China
| | - Sihui Hu
- Department of General surgery, Inner Mongolia Baogang Hospital, Inner Mongolia, P.R. China
| | - Zhiqiang Han
- Department of General surgery, Inner Mongolia Baogang Hospital, Inner Mongolia, P.R. China
| | - Xuejun Jiang
- Department of General surgery, Inner Mongolia Baogang Hospital, Inner Mongolia, P.R. China.
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30
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Transcriptomics-Based Phenotypic Screening Supports Drug Discovery in Human Glioblastoma Cells. Cancers (Basel) 2021; 13:cancers13153780. [PMID: 34359681 PMCID: PMC8345128 DOI: 10.3390/cancers13153780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Glioblastoma (GBM) remains a particularly challenging cancer, with an aggressive phenotype and few promising treatment options. Future therapy will rely heavily on diagnosing and targeting aggressive GBM cellular phenotypes, both before and after drug treatment, as part of personalized therapy programs. Here, we use a genome-wide drug-induced gene expression (DIGEX) approach to define the cellular drug response phenotypes associated with two clinical drug candidates, the phosphodiesterase 10A inhibitor Mardepodect and the multi-kinase inhibitor Regorafenib. We identify genes encoding specific drug targets, some of which we validate as effective antiproliferative agents and combination therapies in human GBM cell models, including HMGCoA reductase (HMGCR), salt-inducible kinase 1 (SIK1), bradykinin receptor subtype B2 (BDKRB2), and Janus kinase isoform 2 (JAK2). Individual, personalized treatments will be essential if we are to address and overcome the pharmacological plasticity that GBM exhibits, and DIGEX will play a central role in validating future drugs, diagnostics, and possibly vaccine candidates for this challenging cancer. Abstract We have used three established human glioblastoma (GBM) cell lines—U87MG, A172, and T98G—as cellular systems to examine the plasticity of the drug-induced GBM cell phenotype, focusing on two clinical drugs, the phosphodiesterase PDE10A inhibitor Mardepodect and the multi-kinase inhibitor Regorafenib, using genome-wide drug-induced gene expression (DIGEX) to examine the drug response. Both drugs upregulate genes encoding specific growth factors, transcription factors, cellular signaling molecules, and cell surface proteins, while downregulating a broad range of targetable cell cycle and apoptosis-associated genes. A few upregulated genes encode therapeutic targets already addressed by FDA approved drugs, but the majority encode targets for which there are no approved drugs. Amongst the latter, we identify many novel druggable targets that could qualify for chemistry-led drug discovery campaigns. We also observe several highly upregulated transmembrane proteins suitable for combined drug, immunotherapy, and RNA vaccine approaches. DIGEX is a powerful way of visualizing the complex drug response networks emerging during GBM drug treatment, defining a phenotypic landscape which offers many new diagnostic and therapeutic opportunities. Nevertheless, the extreme heterogeneity we observe within drug-treated cells using this technique suggests that effective pan-GBM drug treatment will remain a significant challenge for many years to come.
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Differential Regulation of Cellular FAM111B by Human Adenovirus C Type 5 E1 Oncogenes. Viruses 2021; 13:v13061015. [PMID: 34071532 PMCID: PMC8227810 DOI: 10.3390/v13061015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
The adenovirus type 5 (HAdV-C5) E1 transcription unit encodes regulatory proteins that are essential for viral replication and transformation. Among these, E1A and E1B-55K act as key multifunctional HAdV-C5 proteins involved in various steps of the viral replication cycle and in virus-induced cell transformation. In this context, HAdV-C5-mediated dysregulations of cellular factors such as the tumor suppressors p53 and pRB have been intensively investigated. However, cellular components of downstream events that could affect infection and viral transformation are widely unknown. We recently observed that cellular FAM111B is highly regulated in an E1A-dependent fashion. Intriguingly, previous reports suggest that FAM111B might play roles in tumorigenesis, but its exact functions are not known to date. Here, we set out to investigate the role of FAM111B in HAdV-C5 infections. We found that (i) FAM111B levels are upregulated early and downregulated late during infection, that (ii) FAM111B expression is differentially regulated, that (iii) FAM111B expression levels depend on the presence of E1B-55K and E4orf6 and that (iv) a FAM111B knockdown increases HAdV-C5 replication. Our data indicate that FAM111B acts as an anti-adenoviral host factor that is involved in host cell defense mechanisms in productive HAdV-C5 infection. Moreover, these findings suggest that FAM111B might play an important role in the host antiviral immune response that is counteracted by HAdV-C5 E1B-55K and E4orf6 oncoproteins.
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Kawasaki K, Nojima S, Hijiki S, Tahara S, Ohshima K, Matsui T, Hori Y, Kurashige M, Umeda D, Kiyokawa H, Kido K, Okuzaki D, Morii E. FAM111B enhances proliferation of KRAS-driven lung adenocarcinoma by degrading p16. Cancer Sci 2020; 111:2635-2646. [PMID: 32418298 PMCID: PMC7385341 DOI: 10.1111/cas.14483] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/07/2020] [Accepted: 05/10/2020] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is a common type of cancer that represents a health problem worldwide; lung adenocarcinoma (LUAD) is a major subtype of lung cancer. Although several treatments for LUAD have been developed, the mortality rate remains high because of uncontrollable progression. Further biological and clinicopathological studies are therefore needed. Here, we investigated the role of family with sequence similarity 111 member B (FAM111B), which is highly expressed in papillary-predominant LUAD; however, its role in cancer is unclear. An immunohistochemical analysis confirmed that papillary-predominant adenocarcinomas exhibited higher expression of FAM111B, compared with lepidic-predominant adenocarcinomas. Additionally, FAM111B expression was significantly correlated with clinical progression. In vitro functional analyses using FAM111B-knockout cells demonstrated that FAM111B plays an important role in proliferation and cell cycle progression of KRAS-driven LUAD under serum-starvation conditions. Furthermore, FAM111B regulated cyclin D1-CDK4-dependent cell cycle progression by degradation of p16. In summary, we revealed the clinical importance of FAM111B in human tumor tissues, as well as its function as a degradative enzyme. Therefore, FAM111B has potential as a clinicopathological prognostic marker for LUAD.
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Affiliation(s)
- Keisuke Kawasaki
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Sachiko Hijiki
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kenji Ohshima
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takahiro Matsui
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yumiko Hori
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masako Kurashige
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Daisuke Umeda
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroki Kiyokawa
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kansuke Kido
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Research Institute for Microbial Diseases, Genome Information Research Center, Osaka University, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
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